Something must have changed – what about deleting all the files on the server & republishing them?
You might also try the Source Control forum – lots of Sharepoint discussions over there
quite frankly, that solution terrifies me but thanks :-)
Mmmh. Did you update SharePoint or change the authentication structure?
The easiest way to publish is simply to map a document library as a network drive. You can then publish to a network drive and let Windows handle the SharePoint quircks